Ewan Birney

NAME

Bio::SearchIO::Writer::HTMLResultWriter - Object to implement writing a Bio::Search::ResultI in HTML.

SYNOPSIS

  use Bio::SearchIO;
  use Bio::SearchIO::Writer::HTMLResultWriter;

  my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

  my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
  my $out = new Bio::SearchIO(-writer => $writer);
  $out->write_result($in->next_result);

DESCRIPTION

This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter();
 Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object 
 Returns : Bio::SearchIO::Writer::HTMLResultWriter
 Args    :

remote_database_url

 Title   : remote_database_url
 Usage   : $obj->remote_database_url($type,$newval)
 Function: This should return or set a string that contains a %s which can be
           filled in with sprintf.
 Returns : value of remote_database_url
 Args    : $type - 'PROTEIN' or 'P' for protein URLS
                   'NUCLEOTIDE' or 'N' for nucleotide URLS
           $value - new value to set [optional]

to_string

 Purpose   : Produces data for each Search::Result::ResultI in a string.
           : This is an abstract method. For some useful implementations,
           : see ResultTableWriter.pm, HitTableWriter.pm, 
           : and HSPTableWriter.pm.
 Usage     : print $writer->to_string( $result_obj, @args );
 Argument  : $result_obj = A Bio::Search::Result::ResultI object
           : @args = any additional arguments used by your implementation.
 Returns   : String containing data for each search Result or any of its
           : sub-objects (Hits and HSPs).
 Throws    : n/a

id_parser

  Title   : id_parser
  Usage   : $index->id_parser( CODE )
  Function: Stores or returns the code used by record_id to
            parse the ID for record from a string.  Useful
            for (for instance) specifying a different
            parser for different flavours of FASTA file. 
            Returns \&default_id_parser (see below) if not
            set. If you supply your own id_parser
            subroutine, then it should expect a fasta
            description line.  An entry will be added to
            the index for each string in the list returned.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE

default_id_parser

  Title   : default_id_parser
  Usage   : $id = default_id_parser( $header )
  Function: The default Fasta ID parser for Fasta.pm
            Returns $1 from applying the regexp /^>\s*(\S+)/
            to $header.
  Returns : ID string
  Args    : a fasta header line string